Protein Based Memory Storage

SEMINAR REPORT

ON

Protein BasedProtein Based Memory StorageMemory Storage

SUBMITTED BY:

Mr.Amey Vilas Deshpande

SJVPM’s Polytechnic

1

Protein Based Memory Storage

CERTIFICATECERTIFICATE

S.J.V.P.M.’S POLYTECHNICFattechand Marg, Chinchwad, pune-411 033.

This is to certify that student Mr.Amey .V.Deshpande has successfully presented a Seminar on topic

“Protein Based Memory Storage”

Mrs. Tingre S.S. Mrs. Deshpande A.H. Mr. Thite A.B.

Subject Teacher H.O.D PRINCIPAL

SJVPM’s Polytechnic

2

Protein Based Memory Storage

Index

Introduction

Evolution of memory

current Vs latest

Protein based memory

3-dimensional optical memory

Data writing techniques

Data reading techniques

Advantages

New

Conclusion

References

SJVPM’s Polytechnic

3

Protein Based Memory Storage

ABSTRACT

While magnetic and semi-conductor based information storage devices have been in use since the

middle 1950's, today's computers and volumes of information require increasingly more efficient and faster

methods of storing data. While the speed of integrated circuit random access memory (RAM) has increased

steadily over the past ten to fifteen years, the limits of these systems are rapidly approaching

. In response to the rapidly changing face of computing and demand for physically smaller, greater

capacity, bandwidth, a number of alternative methods to integrated circuit information storage have surfaced

recently. Among the most promising of the new alternatives are photopolymer-based devices, holographic

optical memory storage devices, and protein-based optical memory storage using rhodopsin , photosynthetic

reaction centers, cytochrome c, photosystems I and II, phycobiliproteins, and phytochrome.

This paper focuses mainly on protein-based optical memory storage using the photosensitive

protein bacteriorhodopsin with the two-photon method of exciting the molecules, but briefly describes

what is involved in the other two. Bacteriorhodopsin is a light-harvesting protein from bacteria that live in

salt marshes that has shown some promise as feasible optical data storage. The current work is to hybridize

this biological molecule with the solid state components of a typical computer. Along with that this paper is

explaining some currently existing projects.

“Internal revolution and External Evolution in Memory Research”

SJVPM’s Polytechnic

4

Protein Based Memory Storage

Introduction:

From the time of homosafien, man has tried to record important events and techniques for everyday

life. At first, it was sufficient to paint on the family cave wall how one hunted. Then came the people who

invented spoken languages and the need arose to record what one was saying without hearing it firsthand.

Therefore, year’s later, more early scholars invented writing to convey what was being said. Pictures gave

way to letters which represented spoken sounds. Eventually clay tablets gave way to parchment, which gave

way to paper. Paper was, and still is, the main way people convey information. However, in the mid

twentieth century computers began to come into general use . . .

Evolution of Memories:

Computers have gone through their own evolution in storage media. In the forties, fifties, and sixties,

everyone who took a computer course used punched cards to give the computer information and store data.

In 1956, researchers at IBM developed the first disk storage system. This was called RAMAC (Random

Access Method of Accounting and Control)

Since the days of punch cards, computer manufacturers have strived to squeeze more data into

smaller spaces. That mission has produced both competing and complementary data storage technology

including electronic circuits, magnetic media like hard disks and tape, and optical media such as compact

disks.

Today, companies constantly push the limits of these technologies to improve their speed, reliability,

and throughput -- all while reducing cost. The fastest and most expensive storage technology today is based

on electronic storage in a circuit such as a solid state "disk drive" or flash RAM. This technology is getting

faster and is able to store more information thanks to improved circuit manufacturing techniques that shrink

the sizes of the chip features. Plans are underway for putting up to a gigabyte of data onto a single chip.

Magnetic storage technologies used for most computer hard disks are the most common and provide

the best value for fast access to a large storage space. At the low end, disk drives cost as little as 25 cents per

megabyte and provide access time to data in ten milliseconds. Drives can be ganged to improve reliability or

throughput in a Redundant Array of Inexpensive Disks (RAID). Magnetic tape is somewhat slower than

disk, but it is significantly cheaper per megabyte. At the high end, manufacturers are starting to ship tapes

SJVPM’s Polytechnic

5

Protein Based Memory Storage

that hold 40 gigabytes of data. These can be arrayed together into a Redundant Array of Inexpensive Tapes

(RAIT), if the throughput needs to be increased beyond the capability of one drive.

For randomly accessible removable storage, manufacturers are beginning to ship low-cost cartridges

that combine the speed and random access of a hard drive with the low cost of tape. These drives can store

from 100 megabytes to more than one gigabyte per cartridge.

Standard compact disks are also gaining a reputation as an incredibly cheap way of delivering data to

desktops. They are the cheapest distribution medium around when purchased in large quantities ($1 per 650

megabyte disk). This explains why so much software is sold on CD-ROM today. With desktop CD-ROM

recorders, individuals are able to publish their own CD-ROMs.

With existing methods fast approaching their limits, it is no wonder that a number of new storage

technologies are developing. Currently, researches are looking at protein-based memory to compete with the

speed of electronic memory, the reliability of magnetic hard-disks, and the capacities of optical/magnetic

storage. We contend that three-dimensional optical memory devices made from bacteriorhodopsin utilizing

the two photon read and write-method is such a technology with which the future of memory lies.

Current Vs Latest:

The demands made upon computers and computing devices are increasing each year. Processor

speeds are increasing at an extremely fast clip. However, the RAM used in most computers is the same type

of memory used several years ago. The limits of making RAM more dense are being reached. Surprisingly,

these limits may be economical rather than physical. A decrease by a factor of two in size will increase the

cost of manufacturing of semiconductor pieces by a factor of 5.

All Dimms are 12cm by 3cm by 1cm or about 36 cubic centimeters. Whereas a 5 cubic centimeter block of

bacteriorhodopsin studded polymer could theoretically store 512 gigabytes of information. When this

comparison is made, the advantage becomes quite clear. Also, these bacteriorhodopsin modules could also

theoretically run 1000 times faster.

In response to the demand for faster, more compact, and more affordable memory storage devices,

several viable alternatives have appeared in recent years. Among the most promising approaches include

memory storage using holography, polymer-based memory, and our focus, protein-based memory.

SJVPM’s Polytechnic

6

Protein Based Memory Storage

Protein-Based Memory:

There have been many methods and proteins researched for use in computer applications in recent

years. However, among the most promising approaches, and the focus of this paper, is 3-Dimensional

Optical RAM storage using the light sensitive protein bacteriorhodopsin.

Bacteriorhodopsin is a protein found in the purple membranes of several species of bacteria, most

notably Halo bacterium halobium. This particular bacteria lives in salt marshes. Salt marshes have very high

salinity and temperatures can reach 140 degrees Fahrenheit. Unlike most proteins, Bacteriorhodopsin does

not break down at these high temperatures.

Early research in the field of protein-based memories yielded some serious problems with using

proteins for practical computer applications. Among the most serious of the problems was the instability and

unreliable nature of proteins, which are subject to thermal and photochemical degradation, making room-

temperature or higher-temperature use impossible. Largely through trial and error, and thanks in part to

nature's own natural selection process, scientists stumbled upon Bacteriorhodopsin, a light-harvesting

protein that has certain properties which make it a prime candidate for computer applications. While

Bacteriorhodopsin can be used in any number of schemes to store memory, we will focus our attention on

the use of Bacteriorhodopsin in 3-Dimensional Optical Memories.

SJVPM’s Polytechnic

7

Protein Based Memory Storage

BACTERIORHODOPSIN PHOTOCYCLE

Bacteriorhodopsin is a photochemically active protein found in the purple membrane of the

bacteria Halobacterium salinarium, which was known as Halobacterium halobium. The polypeptide

chain is made of seven closely spaced alpha-helical segments looped across the lipid bilayer. The

interhelical space contains the all-trans-retinal chromophore which is linked to lys-216 on helix G

as a protonated Schiff base.

Photochemically active means that it reacts to light. It has a photochemical reaction cycle, or

photocycle. This cycle basically transports protons from inside the cell to outside the cell in the

bacteria Halobacterium halobium. The native photocycle has several spectroscopically unique steps,

bR --> K <--> L <--> M1 --> M2 <--> N <-->O, which occur in a roughly linear order. The bR state

is the protein in its native state and each intermediate is represented by a letter of the alphabet.

However, the important, main photochemical event in this cycle is a trans to cis photoisomerization

around the thirteenth Carbon atom to the fourteenth carbon double bond in the chromophore.

This is the chromophore

At around the temperature of 80 K, the native protein undergoes this photocycle and switches

between a green absorbing state and a red absorbing state. At approximately room temperature, the

protein switches between a green absorbing state and a blue absorbing state. In both the ground

SJVPM’s Polytechnic

8

Protein Based Memory Storage

(green) and excited (red or blue) states, the chromophore displays several metastable configurations.

The main event follows these steps:

1. A change in the shape of the conformational potential energy surface

resulting from electron excitation

2. A conformational change

3. A non-radiative decay to the ground state

The single critical step in the proton pumping ability of the protein is the transfer of the

Schiff base proton do D85, and piece of the protein, in the L --> M reaction. Absorption of light

leads to rapid photoisomerization in the excited state because the barrier to conformation al change

in that state is negative. In a manner of thinking, the conformational motion of the excited state acts

to gate the conformational motion of the ground state.

In the L state, the Schiff base exhibits strong H-bonding with close water molecules and

distorts the chromophore near the Schiff base. The two necessary coordinators for these water

molecules are the anionic Asp85 and Asp212. That coincides with the Trp182 interacting with the

retinal skeleton by the 9-methyl group. These events bring about the deprotonation of the Schiff

base.

Also in the L intermediate state, the backbone has good local structural flexibility. This is

evidenced by the many different change in the peptide C to O double bond stretching vibrational

frequencies. Some of these frequency variations correlate to the O to H single bond stretching

vibrational frequencies. This indicates that the structural changes can come from changing

interaction with water molecules. A network of H-bonding including bonds between water and

peptides, exists between two pieces of the protein, Asp85 and Asp96. This network exhibits changes

most often in the bR to L transformation, which would be the first step in writing to a block of

bacteriorhodopsin memory.

In the K intermediate, an H-bonding change of the peptide C to O double bond of a valine

residue, called Val49, occurs. This stays on in the L intermediate, but is gone in the M intermediate.

This is affected by a mutation in the protein.

Water appears to affect the C to O double bond affects the protein at specific regions. Some,

which exhibit O to H single bond stretching frequencies, interact with the C to O double bond of the

Val49 piece.

The relative stability of some of the intermediate states determines their usefulness in

computing applications. The initial state of the native protein, often designated bR, is quite stable. SJVPM’s Polytechnic

9

Protein Based Memory Storage

Some of the intermediates are stable at about 80K and some are stable at room temperature, lending

themselves to different types of RAM.

For computers, the two or three most stable states of the protein would be used to record data

in binary form. This is the proposed photocycle for computing needs:

The photocycle for computer memory

An interesting intermediate in the photocycle is the O intermediate. The O intermediate is an

all-trans structure like the native protein state. The native state is a light-adapted state. The O state is

the red absorbing state.

The M state, or unprotonated Schiff base, does not accumulate in the photocycle. This is

strange since this protein transports protons. This could mean two things. The first is that the M

state cannot be observed because the kinetics is set against its build-up. The other is that the Schiff

base does not deprotonate and the transport is based on a completely different mechanism than the

wild type protein. The two kinetic reasons for this lack of M are that the rate of decay of M is faster

than the rate of formation or that the L <--> M and M <--> N equilibrium are tilted away from the

M state

3-Dimensional Optical Memories:

SJVPM’s Polytechnic

10

Protein Based Memory Storage

Three-dimensional optical memory storage offers significant promise for the development of a new

generation of ultra-high density RAMs. One of the keys to this process lies in the ability of the protein to

occupy different three-dimensional shapes and form cubic matrices in a polymer gel, allowing for truly

three-dimensional memory storage. The other major component in the process lies in the use of a two-

photon laser process to read and write data. As discussed earlier, storage capacity in two-dimensional optical

memories is limited to approximately 1/lambda2 (lambda = wavelength of light), which comes out to

approximately 108 bits per square centimeter. Three-dimensional memories, however, can store data at

approximately 1/lambda3, which yields densities of 1011 to 1013 bits per cubic centimeter. The memory

storage scheme which we will focus on, proposed by Robert Birge in Computer (Nov. 1992), is designed to

store up to 18 gigabytes within a data storage system with dimensions of 1.6 cm * 1.6 cm * 2 cm. Bear in

mind, this memory capacity is well below the theoretical maximum limit of 512 gigabytes for the the same

volume (5-cm3).

Data Writing Technique:

Bacteriorhodopsin, after being initially exposed to light (in our case a laser beam), will change to

between photo isomers during the main photochemical event when it absorbs energy from a second laser

beam. This process is known as sequential one-photon architecture, or two-photon absorption. While early

efforts to make use of this property were carried out at cryogenic temperatures (liquid nitrogen

temperatures), modern research has made use of the different states of bacteriorhodopsin to carry out these

operations at room-temperature.

The process breaks down like this: Upon initially being struck with light (a laser beam), the

bacteriorhodopsin alters its structure from the bR native state to a form we will call the O state. After a

second pulse of light, the O state then changes to a P form, which quickly reverts to a very stable Q state,

which is stable for long periods of time (even up to several years).

The data writing technique proposed by Dr. Birge involves the use of a three-dimensional data storage

system. In this case, a cube of bacteriorhodopsin in a polymer gel is surrounded by two arrays of laser beams

placed at 90 degree angles from each other. One array of lasers, all set to green (called "paging" beams),

activates the photo cycle of the protein in any selected square plane, or page, within the cube. After a few

milliseconds, the number of intermediate O stages of bacteriorhodopsin reaches near maximum. Now the

other set, or array, of lasers - this time of red beams - is fired.

The write process

SJVPM’s Polytechnic

11

Protein Based Memory Storage

The second array is programmed to strike only the region of the activated square where the data bits

are to be written, switching molecules there to the P structure. The P intermediate then quickly relaxes to the

highly stable Q state. We then assign the initially-excited state, the O state, to a binary value of 0, and the P

and Q states are assigned a binary value of 1. This process is now analogous to the binary switching system

which is used in existing semiconductor and magnetic memories. However, because the laser array can

activate molecules in various places throughout the selected page or plane, multiple data locations (known as

"addresses") can be written simultaneously - or in other words, in parallel.

Data Reading Technique:

The system for reading stored memory, either during processing or extraction of a result relies on the

selective absorption of red light by the O intermediate state of bacteriorhodopsin. To read multiple bits of

data in parallel, we start just as we do in the writing process. First, the green paging beam is fired at the

square of protein to be read. After two milliseconds (enough time for the maximum amount of O

intermediates to appear), the entire red laser array is turned on at a very low intensity of red light. The

molecules that are in the binary state 1 (P or Q intermediate states) do not absorb the red light, or change

their states, as they have already been excited by the intense red light during the data writing stage.

The read process

However, the molecules which started out in the binary state 0 (the O intermediate state), do absorb

the low-intensity red beams. A detector then images (reads) the light passing through the cube of memory

and records the location of the O and P or Q structures; or in terms of binary code, the detector reads 0's and

SJVPM’s Polytechnic

12

Protein Based Memory Storage

1's. The process is complete in approximately 10 milliseconds, a rate of 10 megabytes per second for each

page of memory.

Advantages:

Clearly, there are many advantages to protein-based memory, among the most significant being cost,

size, and memory density. However, there are still several barriers standing in the way of mass-produced

protein-based memories. For three-dimensional memory to work, all of the molecules need to be reached

without altering any other molecules. This is done with a process called two-photon interaction.

Single Vs Two Photons:

First, let's consider why we even need to use two photons. Let's try to do this with a single photon. A

chunk of bacteriorhodopsin-laden polymer would be the memory in this example. The source of light in this

example would be a laser of appropriate wavelength to excite the bacteriorhodopsin from the bR to the M or

Q state. As a person was using this computer, the RAM would begin to be used up. The surface of the chunk

of polymer with our favorite protein would slowly get used up. Eventually, the need to use the memory

storage capacity inside the chunk of polymer would arise.

No big deal, you're thinking. Just shine the laser on the molecules inside. the chunk. Okay. Let's try

it. Zap!! we've encoded on the in sided of the chunk. Now, it's time to read the entire RAM for some

computations you need to do for chemistry class. The computer starts reading the RAM and all of a sudden

it can't go any further because the memory has been corrupted. This corruption was due to the use of a single

photon to change the state of the bacteriorhodopsin. A two photon method would reduce this type of

corruption. The two photons would each have only part of the energy needed to change the state of the

bacteriorhodopsin. Therefore they would pass through the polymer until they coincided at a point and

changed a molecule of bacteriorhodopsin. The single photon method would not be a good choice for a three-

SJVPM’s Polytechnic

13

Protein Based Memory Storage

dimensional memory. A single photon would excite all of the molecules that are in its path. If the surface of

the chunk of polymer was used to store something for the computer, that information would be corrupted by

the photon as the computer attempted to write to some of the molecules in the inside of the polymer. The

photon would also excite all of the molecules in its path through the polymer chunk.

Projects:

Bacteriorhodopsin Optical Memory

Purple membrane from Halo bacterium, Halobium.

Bi-stable red/green switch

In protein coat at 77K, 107-108 cycles

10,000 molecules/bit

Switching time, 500 femto seconds

Monolayer fabricated by self-assembly ,Speed currently limited by laser addressing

As an example of current work, consider the molecular optical memory   research underway by Prof.

Robert Birge and his group at Syracuse University. Using the purple membrane from the bacterium Halo

bacterium   Halobium, they've made a working optical bi stable switch, fabricated in a monolayer by self-

assembly, that reliably stores data with 10,000 molecules per bit. The molecule switches in 500 femto

seconds--that's 1/2000 of a nanosecond, and the actual speed of the memory is currently limited by how fast

you can steer a laser beam to the correct spot on the memory.

SJVPM’s Polytechnic

14

Protein Based Memory Storage

Lest you think this is some far out distant future research topic, here's an ad from a couple weeks ago by a

company in West Germany offering bacteriorhodopsin for sale, listing under applications, ``Optical data

processing, optical switches, holography, information processing, nonlinear optics, and light sensors.''

New

Protein based storage...is an experimental means of storing data. Using proteins that respond to light

from bacteria found in salt water, a small cube can store large amounts of data. By using lasers the protein

can be changed depending on various wave lengths, allowing them to store and recall data. As a result

protein can be used to store enormous amounts of data using lasers to read and write binary code. With this

new found technology scientists are now developing a larger more efficient storage media.

The students from Fowler High School, Syracuse New York, have created this presentation with help from

the Living School Book of Syracuse University and the W. M. Keck Center for Molecular Electronics to

show the possibilities of protein memory.

Conclusion:

This paper focuses mainly on protein-based optical memory storage using the photosensitive protein

Bacteriorhodopsin. Bacteriorhodopsin is a light-harvesting protein from bacteria that live in salt marshes

SJVPM’s Polytechnic

15

Protein Based Memory Storage

that has shown some promise as feasible optical data storage. The present research work is to hybridize this

biological molecule with the solid state components of a typical computer.

SJVPM’s Polytechnic

16